Role of Backbone Dipole Interactions in the Formation of Secondary and Supersecondary Structures of Proteins.

ABSTRACT: We present a generic solvated coarse-grained protein model that can be used to characterize the driving forces behind protein folding. Each amino acid is coarse-grained with two beads, a backbone, and a side chain. Although the backbone beads are modeled as polar entities, side chains are hydrophobic, polar, or charged, thus allowing the exploration of how sequence patterning determines a protein fold. The change in orientation of the atoms of the coarse-grained unit is captured by the addition of two oppositely charged dummy particles inside the backbone coarse-grained bead. These two dummy charges represent a dipole that can fluctuate, thus introducing structural polarization into the coarse-grained model. Realistic α/β content is achieved de novo without any biases in the force f

SUBMITTER: Ganesan SJ 

PROVIDER: S-EPMC4053078 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature